For the point cloud registration problem in the vision measurement, a point cloud registration method based on electro-magnetic tracking system is proposed in this paper. First, the measurement and registration systems are built, and coordinate system transformation relation between world coordinate system and transmitter coordinate system is calculated using coordinate system transformation method based on the flat surface. Second, the accurate position and orientation of the receiver relative to the transmitter are used to calculate the transformation relation of transmitter coordinate system and receiver coordinate system. Finally, transmitter coordinate system is taken as intermediate coordinate system. The point cloud from different view can be transformed from world coordinate system to receiver coordinate system, and the point cloud coarse registration is accomplished, then the Iterative Closest Point (ICP) method is used to conduct the fine registration. The registration experiment is conducted using the flat surface with different depth, and the plaster model is also used to verify the registration vision effect. The experiment results show that the registration error of the flat surface is below 0.40 mm after the coarse registration, and the registration error of the flat surface is below 0.04 mm after the fine registration. After the coarse registration, the error of the plaster model can converge quickly when we conduct the fine registration using the ICP method, and the vision effect is good.